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Postdoc position in rapid diagnostics of antimicrobial resistance: Bioinformatics and machine learning

Deadline: 19.04.2020

About the position

Department of Biotechnology, Faculty of Applied Ecology, Agriculture Sciences and Biotechnology, at INN University invites applications from outstanding candidates for a two and a half year (with possibility of extension) postdoc fellowship within the project “AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance”, which is funded by the Research Council of Norway (RCN), Better Health and Quality of Life (BEDREHELSE) program.

Inland Norway University of Applied Sciences

Inland Norway University of Applied Sciences (INN University) is home to over 14,000 students and 1,000 employees, and has campuses in Lillehammer, Hamar, Elverum, Rena, Evenstad and Blæstad.


INN University aspires to build strong and enduring academic and research environments that will spearhead regionally, nationally and internationally. We are developing a new and better institution with high academic and pedagogical quality, aiming at achieving university accreditation by 2020.

Our vision is "Stronger Together".


About the department


The Department of Biotechnology is composed of 23 faculty and staff members. We provide instruction for the PhD-programme in Applied Ecology and Biotechnology, our highly successful Master’s programme in Applied & Commercial Biotechnology and a one-year add-on programme in biotechnology that allows students to qualify for our Master’s programme; exchange students from the EU's Erasmus programme also enrol in modules of the one-year programme.


Department of Biotechnology is part of the NCE Heidner Biocluster, and we are collaborating closely with several Heidner companies, especially within animal and plant breeding. The research profiles of Department of biotechnology can be roughly divided into four core areas:

Reproduction biotechnology, focusing on technological and biological approaches to reveal factors affecting fertility across species and kingdoms. Gametes from animals, aquatic organisms and plants are characterized to identify phenotypic traits important to fertilizing capacity.


Molecular Genetics in Diagnostics, Breeding and Wildlife Management, focusing on functional genomics and development of new DNA technologies for genotyping animals, plants, humans and microbes associated with them.


Biodiscovery, focusing on production and conversion of renewable biological resources and rest raw materials to value added products by fermentation, pre-treatment and extraction, purification of proteins and other biologicals, and enzyme-based biomass conversion.


Bioinformatics focusing on analysis and interpretation of omics data, through a combination of bioinformatics and machine learning tools and algoritms. Our special field of interest is early diagnostics of antimicrobial resistance. Also, bioinformatics plays a central role in a number of our other projects.

The project leader of AMR-Diag, associate professor Rafi Ahmad is the leader of the Bioinformatics and Biodiscovery (B&B) research group at INN. AMR-Diag is a joint Indo-Norwegian researcher project on antimicrobial resistance, following up the bilateral agreement of Science and Technology between India and Norway, and the Memorandum of Understanding on health research between the Indian Council of Medical Research (ICMR) and the Research Council of Norway.

The selected candidate will work in close collaboration with researchers, PhD’s and PostDoc’s from Norwegian and Indian partners.

AMR-Diag project summary and objectives

The emergence and spread of antibiotic resistant (ABR) bacteria is defined as a global health problem by the World Health Organization (WHO). The situation is at its gravest in low and middle-income countries (including India), where antibiotic consumption is high and largely unregulated. In Europe, an estimated 33,000 patients die annually from ABR bacteria. Treating resistant infections results in extra costs and productivity losses, for e.g., in USA an estimated $21 - $34 billion and in Europe €1.5 billion annually. Despite Norway having amongst the lowest use of antibiotics in all of Europe, there has been a recent increase in reported cases for various ABR infections.

Lack of rapid point-of-care diagnostic tests is central to this problem, as studies show that up to 70% of antibiotics are prescribed incorrectly. This is due to physicians not being able to diagnose patients accurately in real-time, leading to prescription of antibiotics for viral infections, or prescription of broad-spectrum antibiotics that should ideally be kept in reserve.

Taking advantage of the advances in real-time whole genome sequencing, bioinformatics, proteomics and machine learning methods we plan to develop a decision-making tool, for the detection of bacterial infection, including its resistance profile. The developed tool will be evaluated on clinical samples from hospitals in India and Norway. AMR-Diag tool will be designed for use by doctors and other health care professionals, providing information needed in order to choose the best treatment. Thereby, resulting in more prudent and appropriate use of antibiotics.

The AMR-Diag project includes national reference centers and lead institutions of AMR research in Norway and India, as well as prominent international collaborators. The proposed AMR-Diag project collaboration will strengthen the already on-going research activities in each involved research group and contribute significant to added value to these on-going activities. Project partners include:

Norwegian partners: Oslo University Hospital (Ullevål), Norwegian Institute of Public Health (FHI) and National Advisory Unit on Detection of Antimicrobial Resistance (K-res), University of Tromsø;

Indian partners: All India Institute of Medical Sciences - Delhi, Indian Institute of Technology - Delhi and Indian Council of Medical Research;

International partners: University of Southampton, Uppsala University, KTH Royal Institute of Technology, Stockholm.

Further information

For more information about the position please contact

Qualifications

At the time of taking up the appointment, the applicant should have completed an PhD degree in the areas of bioinformatics, computational biology, computer science or another relevant scientific discipline.

Required qualifications

  • Exposure to large scale data analysis, preferably whole genome sequence data.
  • Experience in advanced machine learning/deep learning methods including Neural Networks.
  • Experience with programming and use of MATLAB.
  • Fluency in programming languages and scripting in Python and R.

Desired qualifications

  • Knowledge about infection biology and antibiotic resistance.
  • Hands-on experience and demonstrated proficiency with the entire sequencing workflow, from sample preparation to bioinformatic analysis.
  • Experience with algorithm and/or software development
  • Mathematical or statistical modelling in biological data.
  • Hands-on experience with shell script and Linux system

The candidate will also have to demonstrate an excellent level of spoken and written English, possess good interpersonal and communication skills and show willingness to work as part of an international multidisciplinary team.

How to apply

The application and all attachments are to be submitted electronically and should include the following:

  • Application letter
  • CV (education, positions and academic work)
  • Copies of educational certificates and list of references
  • A complete list of publications

Inland Norway University of Applied Sciences aims to achieve a balanced gender composition in the workforce and to recruit people with ethnic minority backgrounds.

According to the Norwegian Law "Offentlighetsloven §25.2 ledd", information about the applicant can be published even if the applicant has requested not to be included in the public list of applicants.

We offer

A position remunerated according to code 1352, post doctor. Previous work experience will be taken into account when deciding placement on the salary scale. Personal insurance is included. A percentage of the salary will be deducted each month as an obligatory premium to the Norwegian Public Service Pension Fund. In addition, there is a matching contribution from the employer to the pension fund.

In addition, we offer

  • Access to state-of-the-art bioinformatics infrastructure, including access to Norwegian supercomputer.
  • Opportunity to work in collaboration, with Oslo University Hospital which one of the world's largest hospitals, and the largest in Northern Europe.
  • An academically stimulating work environment with engaging colleagues in a critical, expanding and prioritized area of research.
  • Working in a multidisciplinary team including bioinformaticians, computer scientists, medical doctors, micro- and molecular biologists.
  • Working in a bilateral Indo-Norwegian project with huge potential.
  • Work in collaboration with PhD students and PostDocs from India.
  • Working on an area critical for public health worldwide.
  • Short stays at partner institutions in India and potentially other partner institutions.
  • An attractive place to live, with immediate access to nature, urban environments and a variety of culture and sport opportunities.
  • Good welfare benefits.

Appointment Conditions

The appointment will be made in accordance with the regulations in force concerning Norwegian State Employees and Civil Servants.

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